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Sexual arousal is thought to be the result of two levels of processing: conscious and unconscious. Whereas some research exists on the neural correlates related with conscious exposure to sexual stimuli, there are no parallel data regarding unconscious or subliminal exposure to such stimuli. In the present study, we therefore compared brain activation of 39 participants (20 women) as they were exposed to supraliminal vs subliminal sexual stimuli. Supraliminal exposure was associated with greater activation in areas that were previously associated with sexual arousal (e.g. caudate nucleus and thalamus) as well as areas that were previously associated with control (e.g. orbitofrontal cortex and cingulate cortex). In contrast, subliminal exposure was mainly related to activation in areas previously associated with sexual arousal. Men and women exhibited theoretically meaningful differences in patterns of activation associated with supra- and subliminal exposure. Findings are discussed with regard to sexual arousal and regulatory processes.